The healthy human microbiome

By Jason Lloyd-Price, Galeb Abu-Ali, Curtis Huttenhower. 2016

1,641 citations recorded by the source corpus.

Humans are virtually identical in their genetic makeup, yet the small differences in our DNA give rise to tremendous phenotypic diversity across the human population. By contrast, the metagenome of the human microbiome—the total DNA content of microbes inhabiting our bodies—is quite a bit more variable, with only a third of its constituent genes found in a majority of healthy individuals. Understanding this variability in the “healthy microbiome” has thus been a major challenge in microbiome research, dating back at least to the 1960s, continuing through the Human Microbiome Project and beyond. Cataloguing the necessary and sufficient sets of microbiome features that support health, and the normal ranges of these features in healthy populations, is an essential first step to identifying and correcting microbial configurations that are implicated in disease. Toward this goal, several population-scale studies have documented the ranges and diversity of both taxonomic compositions and functional potentials normally observed in the microbiomes of healthy populations, along with possible driving factors such as geography, diet, and lifestyle. Here, we review several definitions of a ‘healthy microbiome’ that have emerged, the current understanding of the ranges of healthy microbial diversity, and gaps such as the characterization of molecular function and the development of ecological therapies to be addressed in the future.

Subfields: Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

1. T. Sampson
2. B. Goodman
3. Abdo Hassoun
4. Daniel H. Geschwind
5. J. Durack
6. S. Lynch
7. H. Gardner
8. J. Patra

Citations in the corpus

• Benefaction of probiotics for human health: A review (2018, background): “Notable age-specific compositional shifts reported in gut microbiota composition include a decrease in the Bacteroidetes/Firmicutes ratio and a marked decrease in bifidobacteria in people aged > 60 years, around the time that the immune system starts to decline [7].”
• Human gut microbiota in health and disease: Unveiling the relationship (2022, background): “It has been challenging to define an appropriate healthy microbiome composition because of inter-individual variation (Lloyd-Price et al., 2016).”
• The Central Nervous System and the Gut Microbiome (2016, background): “Hence, this period of life is critical for the establishment of a healthy, stable microbiome (Lloyd-Price et al., 2016; Yatsunenko et al., 2012).”
• A new antibiotic selectively kills Gram-negative pathogens (2019, neutral): “Interestingly, the compound was also largely inactive against gut commensals, including Bacteroides, the main group of Gram-negative symbionts 13 .”
• Species-level functional profiling of metagenomes and metatranscriptomes (2018, neutral): “It has the potential to characterize the extensive biochemical “dark matter” observed in many communities 1 , as well as to link specific molecular activities to environmental 2 and health-associated 3 phenotypes.”
• The Human Gut Microbiome: From Association to Modulation. (2018, neutral): “However, while some disease statesmay be associated with specific microbiome signatures, microbiome states that are unequivocally ‘‘healthy’’ across cohorts are yet to be established (Lloyd-Price et al., 2016).”
• The microbiome and cancer (2018, background): “The geographical focus of the study may make it challenging to generalize the findings [90].”